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Crystal Structure of Epstein-Barr virus gp42 protein
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KG0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 9.5 298 30% PEG-3000, 100 mM CHES pH 9.5, 10 mM YCl3, 25 mM tris pH 7.5, 150 mM NaCl, temperature 298K, VAPOR DIFFUSION
Crystal Properties Matthews coefficient Solvent content 2.01 38.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.792 α = 90 b = 67.469 β = 90 c = 79.463 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD MARMOSAIC 300 mm CCD 2007-03-26 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID APS 22-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.4 46.73 99.4 14237 14139 4.4 4.4
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.4 2.49 99.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1KG0 2.4 46.73 14237 13445 629 99.55 0.21666 0.21548 0.215 0.24226 0.2447 RANDOM 37.86
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -3.99 -2.34 6.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.37 r_dihedral_angle_4_deg 38.216 r_dihedral_angle_3_deg 19.621 r_dihedral_angle_1_deg 7.13 r_scangle_it 4.939 r_mcangle_it 4.342 r_scbond_it 3.308 r_mcbond_it 2.778 r_angle_refined_deg 1.708 r_mcbond_other 0.794
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.37 r_dihedral_angle_4_deg 38.216 r_dihedral_angle_3_deg 19.621 r_dihedral_angle_1_deg 7.13 r_scangle_it 4.939 r_mcangle_it 4.342 r_scbond_it 3.308 r_mcbond_it 2.778 r_angle_refined_deg 1.708 r_mcbond_other 0.794 r_symmetry_vdw_refined 0.225 r_xyhbond_nbd_refined 0.215 r_symmetry_vdw_other 0.202 r_nbtor_refined 0.183 r_nbd_other 0.18 r_symmetry_hbond_refined 0.168 r_nbd_refined 0.163 r_nbtor_other 0.159 r_chiral_restr 0.116 r_bond_refined_d 0.026 r_gen_planes_refined 0.009 r_gen_planes_other 0.005 r_bond_other_d r_angle_other_deg r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2318 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling